3. ouch: phylogenetic comparative analysis- ouch is an R package for phylogenetic comparative analysis based on an explicit modeling approach in which quantitative characters evolve according to a multiple-optimum Ornstein-Uhlenbeck process.

6. NMF - Nonnegative Matrix Factorization- This package provides a flexible framework to perform Non-negative Matrix Factorization (NMF).
It implements a set of already published algorithms and seeding methods, and provides a framework
to test, develop and plug new/custom algorithms.

7. simecol - Ecological Models with R- simecol allows to implement ecological models (ODEs, IBMs, ...) using a template-like object-oriented stucture. It helps to organize scenarios and may also be useful for other areas.

10. PhyloConductor- PhyloConductor aims to form a collection of R packages for phylogenetic, comparative, and other evolutionary analysis that is coherent and user-accessible. Initially we focus on comparative phylogenetic methods for the analysis of trait evolution.

13. TopKLists- The package includes tools for inference, aggregation, and visualization of multiple ranked lists. Consolidated information from two or more such lists comprising the same set of objects can be obtained. Incomplete rankings and partial lists are allowed.